FoldEco: A Model for Proteostasis in E. coli

Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.
Cell Reports (Impact Factor: 8.36). 03/2012; 1(3):265-76. DOI: 10.1016/j.celrep.2012.02.011
Source: PubMed


To gain insight into the interplay of processes and species that maintain a correctly folded, functional proteome, we have developed a computational model called FoldEco. FoldEco models the cellular proteostasis network of the E. coli cytoplasm, including protein synthesis, degradation, aggregation, chaperone systems, and the folding characteristics of protein clients. We focused on E. coli because much of the needed input information--including mechanisms, rate parameters, and equilibrium coefficients--is available, largely from in vitro experiments; however, FoldEco will shed light on proteostasis in other organisms. FoldEco can generate hypotheses to guide the design of new experiments. Hypothesis generation leads to system-wide questions and shows how to convert these questions to experimentally measurable quantities, such as changes in protein concentrations with chaperone or protease levels, which can then be used to improve our current understanding of proteostasis and refine the model. A web version of FoldEco is available at

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Available from: Lila M Gierasch, Jan 29, 2014
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    • "This dramatic catalysis of folding is biologically highly relevant. About 30%–50% of the obligate GroEL substrates, including DapA, share the TIM-barrel domain fold (Fujiwara et al., 2010; Kerner et al., 2005), and many of these proteins aggregate or are degraded in E. coli cells when GroEL/ES is depleted (Calloni et al., 2012; Kerner et al., 2005; Powers et al., 2012). At physiological temperature (37 C), "
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    ABSTRACT: The GroEL/ES chaperonin system functions as a protein folding cage. Many obligate substrates of GroEL share the (βα)8 TIM-barrel fold, but how the chaperonin promotes folding of these proteins is not known. Here, we analyzed the folding of DapA at peptide resolution using hydrogen/deuterium exchange and mass spectrometry. During spontaneous folding, all elements of the DapA TIM barrel acquire structure simultaneously in a process associated with a long search time. In contrast, GroEL/ES accelerates folding more than 30-fold by catalyzing segmental structure formation in the TIM barrel. Segmental structure formation is also observed during the fast spontaneous folding of a structural homolog of DapA from a bacterium that lacks GroEL/ES. Thus, chaperonin independence correlates with folding properties otherwise enforced by protein confinement in the GroEL/ES cage. We suggest that folding catalysis by GroEL/ES is required by a set of proteins to reach native state at a biologically relevant timescale, avoiding aggregation or degradation.
    Full-text · Article · May 2014 · Cell
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    • "The analysis showed that both Lon protease and GroEL/ES chaperonins act on the compact molten globule (MG)-like equilibrium-folding intermediates of DHFR (Ionescu et al., 2000; Ptitsyn, 1995). Based on these findings, we developed a simple quantitative ''triage''like (Gottesman et al., 1997; Powers et al., 2012; Wickner et al., 1999) kinetic model in which cytoplasm is viewed as an active steady-state medium under constant energy and material flow, rather than an equilibrated solution of proteins' thermodynamic states. The model predicts that the effect of mutations on protein abundance and fitness in active cytoplasm is fundamentally different from that in equilibrium in vitro. "
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    ABSTRACT: What are the molecular properties of proteins that fall on the radar of protein quality control (PQC)? Here we mutate the E. coli's gene encoding dihydrofolate reductase (DHFR) and replace it with bacterial orthologous genes to determine how components of PQC modulate fitness effects of these genetic changes. We find that chaperonins GroEL/ES and protease Lon compete for binding to molten globule intermediate of DHFR, resulting in a peculiar symmetry in their action: overexpression of GroEL/ES and deletion of Lon both restore growth of deleterious DHFR mutants and most of the slow-growing orthologous DHFR strains. Kinetic steady-state modeling predicts and experimentation verifies that mutations affect fitness by shifting the flux balance in cellular milieu between protein production, folding, and degradation orchestrated by PQC through the interaction with folding intermediates.
    Full-text · Article · Dec 2012 · Molecular cell
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    ABSTRACT: Much work in recent years has been devoted to understanding the complex process of protein aggregation. This review looks at the earliest stages of aggregation, long before the formation of fibrils that are the hallmark of many aggregation-based diseases, and proposes that the first steps are controlled by the reconfiguration dynamics of the monomer. When reconfiguration is much faster or much slower than bimolecular diffusion, then aggregation is slow, but when they are similar, aggregation is fast. The experimental evidence for this model is reviewed and the prospects for small molecule aggregation inhibitors to prevent disease are discussed.
    Full-text · Article · Oct 2012 · Molecular BioSystems
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